Changing of the Guard
by SGAFan
Summary: SPOILERS FOR 4x03 REUNION! Change comes. Words of advice from one commander of Atlantis to another.


_**Changing of the Guard**_

_**Missing Scene Story between Reunion and Doppelganger**_

Sam paused in the doorway to Dr. Weir's… to **her** office. She sighed deeply. No one on this base would ever accept her as their commanding officer unless she first accepted it herself.

Proceeding into the office, she rounded the desk and stopped again. The décor was sparse. Her own things wouldn't arrive until the Daedalus' next docked, and without them, she could almost hear echoes from the walls of the past three years: decisions made, laughter joined and sorrow shared.

She thought back to the brief time that Dr. Weir had commanded the SGC and smiled. Elizabeth had stepped in and made the role her own so effortlessly… or at least it seemed effortless on the surface. Slowly, Sam sat down and stared for a moment at the closed laptop on the desk while her mind wandered. Could she command here? Would they accept her? She'd already seen the hurt, anger and distrust in Ronon's eyes, but he seemed the type who wore such things close to the surface. Did the rest feel the same? Feel that the IOA had written Elizabeth off before it was time? She knew Sheppard still believed they could rescue her. Sam sighed, remembering the pain and frustration in his eyes when she'd denied his request to mount a rescue. He'd had no feasible plan and they'd both known it. She grimaced and wondered if they thought she was being hastily shoved upon them. Sure, Sheppard and, of course, McKay had been cordial and welcoming when she'd arrived, but what was on the surface wasn't necessarily what they felt.

She looked up at the sound of someone in the doorway clearing his throat and managed a small smile for McKay. "What can I do for you, Rodney?" Her gaze narrowed slightly at his stiff manner.

He slowly walked into the office and stared at her uncertainly for a moment, before holding out a small pin drive. "I, uhh…. I need to give this to you."

Sam cocked her head slightly before reaching out and taking the device. "Okay. Can I ask what it is?" She let the silence between them linger while Rodney looked everywhere except at her. "McKay?"

"It's something Elizabeth…," his voice cracked, "she asked me to hold onto it for her." He took a quick, deep breath. "It's not that she was ever in danger…." His voice trailed off and he squeezed his eyes shut as his shoulders sagged. "I mean…."

"Its okay, Rodney." Sam felt a rare moment of compassion for him. "I get it."

He took a deep breath and opened his eyes, still not quite looking at her. "Elizabeth wanted her successor to have it, if it ever came to that." He chortled bitterly. "She always thought it would be squabbling bureaucrats that'd get her in the end…."

A slight lump formed in Sam's throat as she heard the pain in Rodney's voice; a pain she could feel permeating the entire base. "Thank you." She kept her voice soft and held the compassion in her expression as she watched Rodney's struggle to keep his emotions in check. After a moment, he nodded once and left hastily.

Sam stared at his retreating back until he disappeared up the control room stairs, before looking down at the USB drive – no more than a couple of inches long – in her hand. Standing, she walked over and closed the office door, before returning to her desk to switch on her laptop and plug the device in. Clicking on the one video file it contained, she sat back and watched as Elizabeth's uncertain smile greeted her gaze.

"_Hello." Elizabeth sighed. "Well, I have to say this is a little awkward, considering I don't even know who you are or what circumstances put you into my place." She chuckled quietly. "More than likely, the IOA finally got off their collective butts, actually made some sort of decision, and decided to remove me from command." She bowed her head for a moment. "You should know that whatever decision I made that led to this, I will have made with the best interest of my people and Atlantis in mind." Her gaze narrowed slightly. "You should also know that sometimes the right decision isn't the easiest, or the most popular one." _

Sam paused the recording. Ten years in the SGC had shown her that, but she'd never had to deal as directly with the IOA – or, for that matter, any of the bureaucrats who meddled in the Stargate program – as she had to now. Her brows quirked. Just one more thing to add to the list of concerns threatening to keep her up nights from now on….

Reaching out, she pushed play again.

"_I asked Dr. McKay to safeguard this recording for me as I imagine the IOA would be pretty swift removing me once they made up their mind to do it. If you're watching it, then my assumption was correct." Elizabeth paused and took a deep breath. "There are some things you need to know, mostly about the people you're now commanding. I know you've read their files, or at least I assume so…." _

Even filtered through the camera lens, Sam could sense Elizabeth's growing the intensity.

"…_but there is so much more to all of them than their records." A brief smile lifted the corner of her mouth. This is, without a doubt, the finest group of people it has ever been my pleasure to work with." The smile changed into something more knowing. "Of course, whether or not you choose to take note of my opinions on any of them is entirely up to you, but I'm asking you to at least do me the courtesy of listening while I tell you what I've come to know in the three years I've worked with them." Her expression sobered once more. "We've all faced death and danger more than once. Those moments, I believe, truly define a person, and each one of these people met those dangers head on and showed their real colors."_

_Again, she sighed deeply. "Let me start with Lieutenant Colonel John Sheppard, because he's the one whose record probably has your eyebrows arching more than anyone else. The truth is, in your place, I'd be questioning his appointment as well – if I hadn't had the last three years to put my mind at rest. Yes, John __**is**__ unorthodox and headstrong… but he's also, quite simply, a gifted, natural leader. He'll tell you when he thinks you're wrong… but I've learned to at least listen to him, because his instincts have gotten him and his team out of more trouble than you'd ever think possible. He has an uncanny ability to see the world for what it is; no shades of gray, everything black and white." She smiled fondly. "If you have any diplomatic experience, you'll know that oftentimes things aren't that simple, but John has a strong moral compass that he judges everything by, and sometimes in the world of diplomatic ambiguity, that's just what you need when you're trying to make decisions about things you never imagined in your wildest dreams you'd be facing. Listen to John. He's not always right, but he always has good thoughts. He's an amazing leader who's gained the unwavering loyalty of everyone under his command, and even civilians that aren't. That includes Dr. McKay, and if you haven't realized it yet, that's no small feat." She grinned for a moment, before turning serious again. "Gain John's trust and his confidence, and he'll give it to you, completely… and you'll have his staunch support in what's oftentimes a lonely job." _

Again, Sam paused the recording as she thought about her second in command. Unorthodox she could handle. After all, she'd spent eight years on Jack O'Neill's team and in all that time, she'd seen many officers come and go from the SGC. Some moved on to other things, others ended up in caskets. But one thing she did know was that unorthodox suited the Stargate Program just fine. It took an unorthodox officer to deal with a universe that didn't follow military protocols. She smiled slightly. In fact, since she'd been there, she couldn't remember one salute from Sheppard… and that suited her just fine.

She pushed play once more.

"_Teyla Emmagan." Elizabeth's expression was now dominated by respect. "Teyla's quiet strength and wisdom will amaze you. She has such a deep understanding of her people and the plight of all the humans in this galaxy who've spent countless generations as herd animals to the Wraith. I think I came to rely on her insights more than I ever expected to. You'll find she has a high set of standards, honor being one of the most important. Treat her honorably and she will do the same to you." Elizabeth leaned forward a little. "Sheppard was right to choose her for his team. She's proven her worth over and over again. She can be a valuable asset to you if you listen to her… and I encourage you to do just that. You might be surprised what you'll learn." _

This time, Sam smiled as she paused the recording. In some ways, Teyla reminded her of Teal'c. Soft-spoken, but carrying a big stick, both figuratively and literally if necessary. Sam had only met Teyla briefly and she made a mental note to schedule some time with the Athosian to get to know her better.

Once more, she pushed play.

"_Ronon Dex." Elizabeth gave an almost apologetic smile and shook her head. "If you haven't already had a run in with Ronon, I expect it'll happen soon enough." Her smile faded. "By now, I'm sure you've read his file. Ronon has a hard time trusting anyone, but his loyalty is absolute if you earn it." Her gaze narrowed. "In spite of his brusqueness, he's a good man, although it took me a while to see it. I'll admit I was very hesitant initially to allow Sheppard to add him to his team, but I've never once regretted that decision. He's a fierce warrior, and in a galaxy full of unspeakably evil beings where diplomacy doesn't cut any ice, it's sometimes good to have someone like him around, ready to take the fight to them." Again, she struggled to suppress a smile. "And Ronon is always ready. His tenacity as kept him alive in the face of the destruction of his people and against unbelievable odds. His sound grip on life is something we all can learn from. He never gives up and he inspires those around him to keep on going too." She sighed. "Traits like that are hard to come by and should be jealously guarded. He'll sacrifice himself for anyone he cares about, so if it ever comes to that, make sure it's for a damned good reason." _

Again, Sam paused the video, needing time to absorb Elizabeth's words. And, again, she sighed. Sacrificing her own people. It was a decision she hoped she'd never have to make, but she knew all too well that someday it might come to that. Still, having people under her command willing to follow orders like that without question was somehow a comforting thought… even if she realized her relationship with these people wasn't at that point yet.

Her thoughts turned to her brief and less then cordial encounter with Ronon when she'd first arrived. She liked to think they'd managed to find some common ground after they'd worked together to save John and the others from the Wraith, but she hadn't been sure… not until now.

Elizabeth's words rang in her head_: "…a hard time trusting anyone, but his loyalty is absolute if you earn it."_

"Earn it," Sam muttered. "I can do that…." She pushed play.

"_Rodney McKay." Elizabeth bit her lip in an obvious effort not to laugh. "Oh, Rodney. He'll make your ears bleed with his constant griping, but he's nothing short of brilliant. In a career of working with some of the most intelligent people in the world, I don't think a single one of them holds a candle to Rodney. He has thought his way into… and out of so many seemingly impossible situations that I sometimes wonder if anything is beyond him." She paused, "at least I did until Project Arcturus. If there's one thing about Rodney you must be careful about, it's his ego. He's capable of so many things, but not everything, though he'll swears to you he is. Rodney's the one you might have to save from himself…. And if do you ever find yourself in that situation, be prepared to stick to your guns, because he'll debate it to death with you." She pursed her lips. "One more thing. Underneath all the sarcasm, cynicism, and smart remarks lurks a genuine heart. Rodney really is a good person, even if he does his best to disprove that on a routine basis." Her smile returned. "Don't believe him for a second. He's better and braver then he'll ever let you believe him to be."_

Sam found herself returning Elizabeth's smile as she pressed pause once more and leaned back in her chair. Rodney. God she'd hated him when she first met him, and the verdict was still out on him even now, despite having found a way to work together over the past five years, at least at a professional level. But she had to admit he was brilliant.In the three years he'd spent here, he'd done some amazing things. Her smile turned fond. When they'd first met, he'd been a typical narrow-minded lab rat,accusing her of hair-brained – even half-assed – schemes. Yet somewhere along the way, he'd learned that crazy was sometimes the only thing keeping you from certain death. She remembered reading the Atlantis report on how, exactly, they'd escaped the super volcano on Taranus and laughed quietly. _Talk about hair brained…!_

She pushed play and once more listened to Elizabeth's words.

"_There are so many other people on Atlantis that are amazing in their own rights. Dr. Zelenka and Major Lorne to name a couple. But the people I've spoken about are your first line of defense in dealing with the Pegasus Galaxy. Each one of them has different gifts, and if you're as smart as I think you must be to be the new commander here, you'll get to know each of them and listen to them." Elizabeth smiled ruefully. "My command was only as good as the people around me. But me being relieved of command, shouldn't, for one second, reflect on any of them. While they offered me the best of advice, the decisions were ultimately mine. Remember: follow your instincts, even if they don't exactly mesh with the IOA. They're bureaucrats a galaxy away passing second judgment, and you are the here and now. Never let them hamstring you. It's far better to be relieved of duty knowing you did the right thing than to lose someone under your command from indecision." She paused for a long moment, before nodding once. "Good luck."_

The screen went dark. Pushing away from the desk, Sam stood and walked to the window overlooking the Gate Room. She stared down at the inactive gate, still trying to get used to the different design of the Pegasus version.

Never once since she was given command of Atlantis had she considered changes to her senior staff. In each, she saw qualities that she'd come to learn were essential in the Stargate Program. But, somehow, she felt reassured by Elizabeth's words. Not only that she had the right people under her command, but that each of them would give her a fair shake… in time. For now, they needed space to come to terms with losing Weir, but when they were ready, they'd follow her… and she'd be ready to lead them.

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_This story has been bouncing around in my head for a couple months now. The plot bunny finally settled enough to be written. ;) _


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